Knowledge Base

Article ID: 1033 - Last Modified: June 2, 2011

What should I try if Glide doesn't give me reasonable results?

First, you should assess what are "reasonable" results. For Glide SP, scores of -10 or lower usually represent good binding. For some targets (e.g., with shallow active sites), scores of -8 or -9 might be very good. Metalloproteins and Glide XP both tend to produce lower docking scores (-12 to -15 or even less). The cutoff for a "good" score will vary somewhat from system to system, and changing the van der Waals radii scalings can change the scores significantly. To assess the results you should perform some benchmarking for your receptor of interest, docking the native ligand (if there is one), known actives, and decoy sets, in order to gauge the range and meaning of the scores for your particular system. You should always dock the native ligand or known actives, to ensure that Glide is able to select a native pose with a good score before moving on to screening a library of compounds.

If you have trouble docking the native ligand, various parameters can be adjusted to improve the results:

  • Scale back the receptor or ligand van der Waals radii (or both) if the active site is particularly tight (making it more difficult to fit non-native ligands).
  • If your ligands are large, you can try increasing the number of intermediate structures kept (use the Advanced Settings button in the Settings tab).
  • If the native ligand present during Grid Generation is much smaller than other ligands that you are trying to dock, it is possible that the grids need to be increased in size. You can use the Dock ligands with length <= option in the Site tab to adjust the size of the grids.

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles